Magnesium in PDB 7r7j: Crystal Structure of Radd with Adp

All present enzymatic activity of Crystal Structure of Radd with Adp:
3.6.4.12;

The structure of Crystal Structure of Radd with Adp, PDB code: 7r7j was solved by M.A.Osorio Garcia, K.A.Satyshur, J.L.Keck, M.M.Cox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.65 / 2.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.415, 74.449, 109.4, 84.66, 80.03, 82.77
R / Rfree (%)	23.6 / 26.9

The structure of Crystal Structure of Radd with Adp also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Radd with Adp (pdb code 7r7j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Radd with Adp, PDB code: 7r7j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:41.9 occ:1.00 H A:SER38 2.3 40.8 1.0 HD2 A:LYS68 2.6 58.5 1.0 HB2 A:SER38 2.7 43.1 1.0 OG A:SER38 2.8 39.0 1.0 O2B A:ADP601 2.8 33.5 1.0 HA2 A:GLY36 2.9 46.3 1.0 O2A A:ADP601 3.0 45.6 1.0 N A:SER38 3.1 33.5 1.0 CB A:SER38 3.2 35.4 1.0 HG2 A:LYS37 3.3 51.9 1.0 H A:LYS37 3.3 37.0 1.0 HB3 A:LYS68 3.4 47.8 1.0 N A:LYS37 3.5 30.4 1.0 CD A:LYS68 3.5 48.3 1.0 HG A:SER38 3.5 47.4 1.0 O3A A:ADP601 3.6 39.5 1.0 HZ3 A:LYS68 3.7 62.3 1.0 C A:GLY36 3.7 31.4 1.0 CA A:GLY36 3.7 38.1 1.0 PB A:ADP601 3.7 40.2 1.0 CA A:SER38 3.7 30.6 1.0 PA A:ADP601 3.9 38.9 1.0 HD3 A:LYS68 3.9 58.5 1.0 HE2 A:LYS68 3.9 60.4 1.0 H5'1 A:ADP601 4.0 50.3 1.0 HB2 A:LYS68 4.0 47.8 1.0 HB3 A:SER38 4.0 43.1 1.0 O3B A:ADP601 4.1 32.5 1.0 CB A:LYS68 4.1 39.3 1.0 C A:LYS37 4.1 35.2 1.0 CE A:LYS68 4.2 49.9 1.0 CG A:LYS37 4.2 42.7 1.0 CA A:LYS37 4.3 31.8 1.0 HA3 A:GLY36 4.3 46.3 1.0 H A:GLY36 4.3 38.6 1.0 NZ A:LYS68 4.3 51.5 1.0 HA A:SER38 4.3 37.3 1.0 HD23 A:LEU39 4.4 53.6 1.0 H A:LEU39 4.4 41.5 1.0 HG3 A:LYS37 4.4 51.9 1.0 O A:GLY36 4.4 37.3 1.0 O A:HOH730 4.4 35.8 1.0 CG A:LYS68 4.5 48.1 1.0 HE3 A:LYS37 4.5 50.6 1.0 N A:GLY36 4.5 31.7 1.0 HD22 A:LEU39 4.7 53.6 1.0 CB A:LYS37 4.7 34.2 1.0 C A:SER38 4.8 34.9 1.0 HZ1 A:LYS68 4.9 62.3 1.0 HZ2 A:LYS68 4.9 62.3 1.0 HE2 A:LYS37 4.9 50.6 1.0 C5' A:ADP601 4.9 41.4 1.0 N A:LEU39 4.9 34.1 1.0 CD2 A:LEU39 4.9 44.2 1.0 HB3 A:LYS37 4.9 41.6 1.0 O1A A:ADP601 5.0 36.5 1.0 HG3 A:LYS68 5.0 58.3 1.0 O5' A:ADP601 5.0 32.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Radd with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Radd with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:46.6 occ:1.00 H B:SER38 2.4 45.9 1.0 HB2 B:SER38 2.6 45.4 1.0 HA2 B:GLY36 2.8 51.0 1.0 OG B:SER38 2.9 40.7 1.0 O1B B:ADP601 3.0 35.4 1.0 HG B:SER38 3.0 49.4 1.0 CB B:SER38 3.2 37.3 1.0 HD2 B:LYS68 3.2 54.5 1.0 N B:SER38 3.2 37.7 1.0 H5'1 B:ADP601 3.3 67.2 1.0 O5' B:ADP601 3.3 60.7 1.0 H B:LYS37 3.5 50.5 1.0 HE3 B:LYS68 3.5 54.7 1.0 HG2 B:LYS37 3.5 52.4 1.0 HB3 B:LYS68 3.6 58.4 1.0 CA B:GLY36 3.6 42.0 1.0 N B:LYS37 3.6 41.6 1.0 C5' B:ADP601 3.6 55.5 1.0 O1A B:ADP601 3.7 56.1 1.0 H5'2 B:ADP601 3.7 67.2 1.0 C B:GLY36 3.7 43.2 1.0 CA B:SER38 3.8 34.8 1.0 PB B:ADP601 4.0 41.9 1.0 PA B:ADP601 4.0 44.6 1.0 HB3 B:SER38 4.0 45.4 1.0 CD B:LYS68 4.0 45.0 1.0 O3B B:ADP601 4.1 41.1 1.0 HB2 B:LYS68 4.1 58.4 1.0 O3A B:ADP601 4.2 39.5 1.0 CE B:LYS68 4.2 45.1 1.0 HA3 B:GLY36 4.2 51.0 1.0 CB B:LYS68 4.2 48.2 1.0 H B:GLY36 4.3 53.6 1.0 C B:LYS37 4.3 37.6 1.0 H B:LEU39 4.3 40.8 1.0 HZ2 B:LYS68 4.3 56.8 1.0 CG B:LYS37 4.4 43.2 1.0 HA B:SER38 4.4 42.4 1.0 CA B:LYS37 4.5 37.4 1.0 O B:GLY36 4.5 39.8 1.0 N B:GLY36 4.5 44.2 1.0 HE3 B:LYS37 4.6 57.5 1.0 HG3 B:LYS37 4.7 52.4 1.0 HD3 B:LYS68 4.7 54.5 1.0 CG B:LYS68 4.8 44.5 1.0 NZ B:LYS68 4.8 46.8 1.0 C B:SER38 4.8 36.2 1.0 N B:LEU39 4.8 33.5 1.0 HE2 B:LYS68 5.0 54.7 1.0 CB B:LYS37 5.0 41.9 1.0

M.A.Osorio Garcia, K.A.Satyshur, M.M.Cox, J.L.Keck. X-Ray Crystal Structure of the Escherichia Coli Radd Dna Repair Protein Bound to Adp Reveals A Novel Zinc Ribbon Domain. Plos One V. 17 66031 2022.
ISSN: ESSN 1932-6203
PubMed: 35482735
DOI: 10.1371/JOURNAL.PONE.0266031